Defending Her Honour
by Anjirika
Summary: -Complete- John will always defend Elizabeth’s honour, no matter what that entails. –Chapter 1 is a drabble to S3E2 ‘Misbegotten’ – Chapter 2 deals with the 1st half of S3 – Chapter 3&4 take place after ‘The Return 2’ but before ‘Echoes’ PLZ R&R!
1. A Warning

Disclaimer: These characters do not belong to me (though I wish they did… ) I am merely borrowing them for the moment.

Stargate Atlantis

Season III

Sparky Moment

Spoilers for Episode 2: Misbegotten

**Defending her Honour**

He came storming into her office, Elizabeth knew that he was the first one to have an interview with Richard Woolsey and she had an inkling that it might not have gone well. John's whole attitude and demeanour, screamed to her that things had not gone well.

"Just out of-uh-political curiosity," how much trouble is it going to cause you if I knock this Woolsey guy in the head?"

"May I ask, why you'd like to do that?"

"Eh- just an impulse I had really, one I suspect I'm going to have again the next time I see him. He may not even have to say anything "

"I've never seen you like this" She was surprised at his reaction. Why was he acting like this- what happened in that interview?" "What did Woolsey say to you?"

"Besides judging every damn decision you've ever made?"

"John Sheppard are you defending my honour?" She leaned back in her chair.

'Is she flirting with me?' He hesitated, contemplating this before he answered her. "And judging me for agreeing with you,"

"Well, don't be too hard on him." "I think of all the circling wolves, he's the least likely to actually bite." "If fact, he might even convince the others to leave us alone."

"Alright, so-uh-" Sitting down. "No head knocking"

"It's the thought that count." Elizabeth answered after a shrug, a smirk playing across her face.

"I know it's the thought that counts." John agreed leaning back in the chair. "But still, he was- overly harsh."

"Yes, well," Elizabeth sighed. "He is under an incredible amount of stress, like we all are."

"Still, it doesn't give him, or anyone else the right to attack you." John pointed out, still visibly upset.

"I'm a leader John," Elizabeth pointed out diplomatically. "-that gives anyone and everyone the right to attack my decisions."

"Yeah, but not you,"

"Woolsey attacked me?" Elizabeth asked sitting back in her own chair while John leaned on his elbows on her desk. "Me, personally?"

"Yes." John explained, upset. "He said, that the majority of your decisions have been influenced by your emotions."

"My emotions?" Elizabeth was confused now, intrigued also and a little horrified that Woolsey and the IOA thought that she was ruled by her emotions.

"Yes. He and the IOA think that your decisions have led to disastrous consequences and that your decisions have placed this base and the people in danger countless times and…"

"John?" Elizabeth asked, visibly shaken. "What do you think?"

"What do I think? What do I think?" John laughed sarcastically. "I think that they are wrong. I think that they are dead wrong. Elizabeth, I think that you are a great leader, the best leader for this expedition and I sure as hell know that I will not follow anyone else but you."

"Well, you might have to." Elizabeth whispered looking down at her crossed hands.

"What do you mean?" John asked, his heart stopping for a moment and a fear growing in the pit of his stomach.

"As of now, I am under probation from the IOA."

"What does that mean?" John asked, clearly putting two and two together, but Elizabeth could tell that he wanted to hear it from her own mouth.

"That means that depending on how good a report comes from Woolsey, well- let's just say that if I don't get glowing reviews, you might have to follow someone else." She shrugged her shoulders trying to put on a brave face. "They might even have to militarise this expedition because of my mistakes."

"They wouldn't do that!" John stated, false hope leaking through his voice.

"They just might," Elizabeth countered, somber about how the conversation was going and how it was bringing all her fears to the surface. "And I wouldn't have a choice if they did."

"Of course you have a choice Elizabeth," John pointed out. "You're a civilian-"

"Civilians still have to follow the orders of their boss. And the members of the IOA are my bosses."

"But you're in another damn galaxy!" John sated, his anger rising. "If they recalled you, you could refuse to step through the gate, and they wouldn't be able to do a damn thing about it."

"If Atlantis becomes militarized John," Elizabeth countered. "They could forcibly take me away."

"I see."

"Believe me John, I hope that everything works out but-"

"It sounds like you're giving up."

"I am not giving up." Elizabeth argued. "Believe me John Sheppard, there is nothing I would hate more than to be plucked from Atlantis- from you…all….." She shook her head and sighed. "I just have to face the facts….and thank you for defending me."

"Your welcome"

She watched him go, a small smile playing across her face. John Sheppard would always be there for her, she knew that. She knew that no matter what, he would always be there defending her honour and making sure that she was done right by. She knew in her heart that all of the people under her command (with the exception of Kavanagh) would defend her honour- but somehow, the fact that John would defend her so thoroughly and completely, made her feel so much better.

A/N- Another little drabble that I've had on my hard drive forever, only this one has a second part coming. So look for it soon (and by soon I mean when In The Choices We Make is done)...I just felt the need to update some Sparkiness fluff. So please review, I love reviews...and take thet time to read and review the rest of the Sparky drabbles and ficletts that I've recently updated. I love knowing that my works are being read and enjoyed, so please...review!


	2. Horrid Developments

Things from that moment went from bad to worse….

First, they almost lost Atlantis to a power hungry psycho who used a pheromone to nearly take over Atlantis. And then they alerted another enemy to their presence, the Asurans were a real threat that nearly killed her- then John got captured by their old 'friend' Kolya and was fed upon by the wraith….

Elizabeth thanked the stars every day that the Wraith could give back life and John was returned safe and sound and in Rodney's opinion a little younger to Atlantis, but that wasn't where the bad luck stopped.

The very next crisis was when Rodney and his sister ripped a hole in another universe-but thanks to the help of 'Rod' they averted that catastrophe but then her flagship team was caught on a planet and nearly all killed themselves. Then they found an ancient ship travelling between the void of their two galaxies and they rescued them and found that there were real live ancients on board.

Elizabeth thought that this would be a good thing, but it wasn't. The ancients took Atlantis away from them, and then when the Asurans attacked, she helped John, Rodney and Carson steal a jumper to save Woolsey, O'Neill and Atlantis. How they pulled that one off, Elizabeth wasn't sure but it wasn't without sacrifice. All the ancients had been killed by the Asurans and Elizabeth knew then and there that although they had gotten Atlantis back- her luck had finally run out.

Elizabeth wasn't really surprised at the news however, even though she was expecting it, the fact that it was really happening still shocked her to her core and as she sat at her desk with her head in her hands she vehemently wished that she could do something about it.

And that was how John found Elizabeth, her head resting on her clasped hands and her arms resting on her desk. John paused in her open door way and just stared at her for a couple moments realising that something was really, really wrong and as stomach twisted in fear he saw her raise her head and smile sadly at him.

"John," She whispered quietly. "I'm glad you're here." Elizabeth paused and watched as John walked forward with a furrowed brow and concern in his eyes. "We need to talk."

"What is it?" He asked worriedly as he took his customary place on the left corner of her desk. "What's happened?" John watched as Elizabeth closed her eyes ad took a deep breath to regain her composure and when she opened her eyes again he saw tears glistening in them.

"John," Elizabeth began slowly, as though by not admitting this she could make it go away. "I've just received news from the SGC."

'What kind of news?' John wanted to asked, but in his heart he was afraid to ask- so he merely nodded to Elizabeth, indicating to her that she should continue.

"In the data burst that we got from them, I got an encrypted message from the IOA." Elizabeth continued, her voice wavering with emotion. "They have finished their review of my leadership her in Atlantis and…." Elizabeth looked down, her voice breaking with emotion.

"Elizabeth?" John asked worriedly sinking from the corner of her desk to the chair across from her. "Elizabeth what is it?"

"John," Elizabeth began, visibly upset at what she was going to tell him. "They've decided that my leadership skills are lacking and that due to the increased threat of the Asurans they are militarizing Atlantis and I am being recalled to Earth."

"What?" John exclaimed in shock, his blood boiling with fury. "How could they do that- after all you've done-"

"That's exactly it John," Elizabeth interrupted. "They are doing this because of all I've done. And you have to admit John, I have made some pretty huge mistakes in the past couple of months."

"Oh, like the SGC hasn't made an equal number of mistakes-" John retorted sarcastically. "More, actually seeing how they've been around about eight years longer than we have."

"Yes," Elizabeth agreed with a small smile. "But they were never under such scrutiny before- they are now, and they've pulled up their socks. We didn't."

John didn't reply to that, he was to shocked to do anything but lean back into the chair. And in the stunned silence that followed, his mind finally comprehended what was going on, and that Elizabeth- his Elizabeth – was really going to leave Atlantis, possibly forever.

"So…" John began slowly realizing what this meant. "You're leaving."

"Yes." Elizabeth nodded with a frown. "I am."

"What-"

"Does this mean for Atlantis?" Elizabeth finished looking at John. 'For us?' Was her unasked question, "I don't know." She answered honestly. "I do know that with the increased military presence many of the scientists will have to go…"

"Rodney?"

"No." Elizabeth shook her head. "No, the IOA and Caldwell both agreed that Rodney and Zelenka need to stay here."

"Caldwell?" John asked not understanding what Caldwell would have to do with anything.

"He's replacing me."

"He's-?" John could barely get the words out. "How could he-"

"I know."

"I mean- if any one should-" John choked on the fury that was building up in him. "I should…..but Caldwell?"

"Never knew you wanted my chair John," Elizabeth stated softly evoking a strangled and strained laugh from John.

"You know that's not what I meant." John said seriously looking Elizabeth in her eyes.

"I know." Elizabeth replied quietly.

"Does anyone else have to leave?" John asked after a few moments of awkward silence, wondering if Teyla and Ronan will be asked to leave.

"Don't worry John," Elizabeth promised. "The IOA and Caldwell agreed that both Ronan and Teyla have invaluable information about the Wraith, and the Asurans"

"I see……"

They sat in silence for another couple of awkward moments till Elizabeth brought herself to attention and broke the silence telling John that she now needed to go around to Atlantis and break the news to everyone that she was leaving. John merely nodded, understanding that this was something that she would have to do on her own- all the while wishing vehemently that she didn't have to do it at all.

A/N- I know that I said I wans't going to update for a while- but I did. Here it is, Chapter 2, Horrid Developments. Chapter 3 will be up relatively soon- but when, I have no idea- this story isn't my priority right now, but I wanted to upload it. Hope you enjoyed, please review...I love my reviews


	3. A surprise revelation

3.

It was later that night, the Atlantis expedition was subdued, more so than it had ever been. And John, who had been pacing all day- finally decided to talk to Elizabeth again and he found her on their balcony, watching the city sparkle in the night.

"I hate this." She stated turning around to face John whom she felt approach. "I really do."

"So do I." John replied with a sigh, feeling more nervous than he had ever felt in his life. He was about to do something that could save Elizabeth from leaving, and even though it was risky, and even though it would change them forever, he knew that it was the only way that he wasn't going to lose her/

"And it's not just the fact that I'm being replaced." Elizabeth continued.

"No?" John asked, snapping out of his thoughts.

"No!" Elizabeth exclaimed, even more upset than she had been a couple hours earlier. "It's the fact that Atlantis is being militarized. Our goals should remain the same!"

"I agree." John agreed with a sigh before he continued on. "Is that all you hate about this?"

"No." Elizabeth admitted looking down.. "I hate the fact that I'm being recalled to Earth, permanently." Elizabeth explained softly. "I hate that I have to leave you-er-all of you." Elizabeth sighed and sat on the railing and stared at the crescent moon lamenting the fact that she was leaving. "…..if there were only some way I could change their mind- or stay."

"Marry me."

"What?" Elizabeth asked, whirling her head around to look at John, not quite sure on what he said.

"Marry me." John repeated again, more slowly and full of confidence.

"Marry you." Elizabeth echoed softly standing to face him. "You want me to marry you?"

"Yes."

"W-why?"

"Well, if we were married you could stay on Atlantis." John explained logically.

"John that would never work," Elizabeth protested turning away.

"Why not?" John asked, slightly hurt. He had thought that….but he guessed that he had thought wrong.

"Well, for one thing the IOA wouldn't allow it." Elizabeth pointed out, turning to face him again.

"They can't stop family from staying together." John pointed out as well

"We already are family." Elizabeth stated softly. "You that that John."

"I do know that," John agreed, deciding to push this as far as he could. "…but is there anything wrong with trying to keep our family together?"

"No," Elizabeth agreed softly, tears coming to her eyes because she thought that John was only wanted to marry her to keep her on Atlantis not because he- "But marriage isn't just about keeping people together," Elizabeth continued breaking off her train of thought. "…it's about love."

"Well," John began before taking a deep breath in preparation to take the plunge. "….what……………….what if I said that I………that I love you?"

"J-" Elizabeth began to stunned to speak.

"What if I said that I love you and I don't want to loose you?" John asked placing his hand on Elizabeth's shoulders and pulling her closer to him. "What would you say to that?"

"I- I'd say…." She trailed off, barely knowing what to say. The hurt from Simon suddenly flared up again and for a moment she wasn't sure if she could let herself get into that position again. But as she looked into John's eyes and realised what a risk he had taken by telling her how he felt, she knew in her heart that she couldn't abandon him. She would have to take that risk as well. "……I'd say that I love you too." She answered with a smile. "….and I don't want to loose you either."

"Really?" John asked, slightly shocked that Elizabeth had admitted that she loved him.

"Really," Elizabeth assured with a giggle. And she watched as John was so overcome with emotion that he swooped in and kissed her. The kiss seemed to last forever and when they pulled away, they were both breathless. "Wow…" Elizabeth stated with a smile.

"Yeah," John agreed as well. "Wow."

"I've wanted to do that for a long time." Elizabeth admitted, stressing the word 'I've'

"So have I." John agreed pulling Elizabeth into a hug, knowing exactly what she meant. "Elizabeth…"

"Yes John?" Elizabeth asked looking up into his eyes.

"Let's get married."

"Here?" Elizabeth asked with a giggle. "Now?"

"Yes. Here, now."

"But no one in Atlantis can do the ceremony." Elizabeth pointed out, always her logical self.

"I never thought of that." John replied with a groan of frustration. "I could request some leave on Earth, heavens knows that I have enough of it stacked up….." He paused and thought about it. "…we could have a small ceremony."

"I could invite my mum," Elizabeth stated with a small smile. "And you…." She paused and realised that John had never talked about his family to her at all. "Do you have any family?" She asked taking his hand in hers. "I've never heard you speak about them, not in three years….and when we were under siege, you didn't send a message to anyone."

"You're all the family I've ever had" John stated with a smile as he brushed a stray curl from Elizabeth's face. "The only family I'll ever need."

"Oh John…" Elizabeth began, tears rising to her eyes. "That's so…."

"Shh…." John soothed and he swooped in and kissed her again. And together they stayed on their balcony watching the Atlantean sky, knowing that on this night, their entire lives had changed.

A/N- Hey well I know I said that I wouldn't update this for a while, but I got it done on the weekend and I've been trying to upload it all week and FF has been being stubborn- but it's up now, hope you like it, I'm thinking that they'll be one more chapter...oh and I know that this seems a little rushed John suddenly proposing but I think it works- they're not the type of people to take it slow and I'm working under the assumption that they know eachother really well already so the initial dating phase doesn't need to happen... :D Other than that just a chonological note, this story takes place after the Return Part 2 but before Echoes which (I must say) was a totally wonderful Sparky episode. :D Look for the epilogue/conclusion coming soon...I hope.


	4. Time to say goodbye

4. Time to say goodbye

The day of her leaving had arrived and as Elizabeth watched as her belongings were once more packed up and taken through the Stargate she couldn't help but stop, turn and look at the gateroom that had been her home for the past three years.

"Atlantis isn't going to be the same with out you…" John whispered in her ear as he joined her with a duffle-bag over his shoulder.

"…I won't be gone that long…" Elizabeth answered with a girlish smile.

"Elizabeth-"

"Yes Teyla….?" Elizabeth asked turning quickly from John to see the younger Athosian woman standing before her with several other Athosian youths and Ronan behind her.

"May your life on Earth be bountiful and safe…." Teyla wished as one of the young Athosian girls who was behind her presented Elizabeth with a gift wrapped in cloth. Elizabeth took the gift gratefully and gave it to John who tucked it in the top of his duffle bag.

"Thank you Teyla…" Elizabeth thanked as she wrapped the Athosian women up in a hug. "…but you know," she whispered cheekily in her ear. "-I won't be gone that long…"

"Elizabeth?" Teyla began questioningly when Rodney cut in.

"Elizabeth!"

"Yes Rodney…?" Elizabeth asked turning to see Rodney coming down the gateroom stairs. "…what can I do for you?"

"Well I was just going to-" Rodney paused and pointed up to the control room but seemed to lose his train of thought. "-I just-"

"Well Rodney?" Elizabeth asked with a small smile as she walked up to the bumbling scientist. "What is it?"

Whatever Rodney was going to say, he didn't say it. Instead he drew Elizabeth up in an awkward hug and as Elizabeth hugged Rodney back, fierce tears came to her eyes as she realised that this would be the last time that she would see any of them as their leader- maybe forever.

'…hopefully I can convince the IOA that Atlantis needs a negotiator…' Elizabeth whispered silently to herself as she pulled out of Rodney's hug.

"I'll miss you too Rodney-" She whispered quietly into his ear as he too pulled away from her.

"Take care Elizabeth." Rodney stated curtly and while his face didn't betray his feelings she knew that he would miss her terribly too.

"Elizabeth…" John began pulling Elizabeth from Rodney towards the gate. "..it's time for us to go."

"Yes John," Elizabeth answered softly as she grasped his hand- the action not going un-noticed by the people around her. "Just let me say goodbye…"

"Of course…"

Elizabeth smiled as John took a few steps backwards allowing Elizabeth to say her final goodbye to Atlantis and her people. Elizabeth took one last glance around the control room and saw that in addition to those whom she saw most, many others from the expedition came walking forward and she knew that it was finally time to say goodbye.

"Atlantis…this is Elizabeth Weir…" Elizabeth paused and collected herself before continuing, trying her best to keep her voice steady and calm. "…as many of you know, the International Oversight Association has deemed that my leadership has been lacking these last few months and have seen fit to replace me with Colonel Steven Caldwell, thus militarizing Atlantis." Elizabeth paused and watched as Caldwell came to the edge of the balcony while the rest of the Atlantis personal stiffened slightly and Elizabeth knew that she couldn't sabotage Caldwell's leadership.

"I know," She continued with a slight waver in her voice as she brushed a stray curl out of her face. "-I know that you all will award him the greatest respect as you all have been gracious enough to bestow upon me…. But my time has come to say goodbye and I wish you all the best of luck in your trials against the wraith and the Asurans and I hope that we will all meet again one day…"

Elizabeth turned to leave with John at her side when she suddenly got the impulse to add one more final thing.

"…and for those of you in the betting pool…" She continued with a cheeky grin looking at John with love and adoration in her eyes. "…Colonel Sheppard and I will be officially engaged when we are on Earth-"

Elizabeth paused amidst the outcry of hooting and hollering as those who had gravitated to the control room whooped with cheer and congratulations and Elizabeth saw Zelenka make Rodney pay up

"-and you are all welcome to the wedding in three months time-" Elizabeth continued with a smile. "-so until then, goodbye for now…take care of each other, and be safe until I see you all again…..Weir out."

And with that Elizabeth turned off her comm. link, mournfully took it off and placed it in the hands of John who clasped it like it was buried treasure. And then, hand in hand, they went through the Stargate towards Earth and a new future together.

-Fin

* * *

A/N- Short ending I know...and I bet you guys thought that I had forgotten about this story... :D ...well no. It is finished now though, I may do a sequel or continue it but I doubt it. It started as a drabble and expanded into a story...I think that its time to put it to rest now. Thank you for reading, hope you enjoyed it, leave a review if you can and check out my other works... :D 


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